Summary
Understanding the myriad of myeloid subsets and identifying specific and discrete phenotypes is challenging in a human setting. Laboratory models of human myeloid biology lack tissue context, but the differences between common models and in vivo phenotypes have not been systematically evaluated. Here, we assemble a large transcriptional atlas of human myeloid biology representing ~1000 samples, comparing freshly isolated, cultured, and stem-cell derived myeloid cell types. Common myeloid models including pluripotent stem cell-derived macrophages fail to recapitulate developmental or tissue contexts. A shared feature of pluripotent stem cell-derived macrophages is the atypical expression of collagen, in addition to being highly efferocytotic. The resulting iMAC atlas is available at the Stemformatics.org platform, where users can review gene expression as well as upload and benchmark their own samples for comparison against a library of human tissue-resident and laboratory models of macrophage or dendritic cell biology.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Use of the atlas as a classification tool for single cell data in Fig 1, Supp Fig 1. Addition of functional validation of the collagen profile in Fig 4.
https://bitbucket.org/stemformatics/s4m_pyramid/src/master/scripts/atlas.py